[gmx-users] problem with calculating SASA

Maryam Hamzehee maryam_h_7860 at yahoo.com
Mon Jan 30 12:40:32 CET 2012

Dear Gromacs list
I am trying to calculate the surface area for my DNA-protein complex using do_dssp or g_sas. But when I convert the pdb file to *.gro file, the topology file *.top has only protein molecule and DNA is not included, how can I edit the topology file and include DNA in order to be recognizable for the system. I tried the do_dssp but the surface area for DNA has not been calculated. It should be noted that my DNA has double strand consists of 8 nucleotides. Is it necessary to include 2 DNA in molecule type section of topology file? 

Any help in this regard would be highly appreciated.

Best regards,
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